Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE FROM PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA 1448A
 
Authors :  K. N. Rao, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  10 Apr 07  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Deoxyguanosinetriphosphate Triphsphohydrolase, Pseudomonas Syringae Pv. Phaseolicola 1448A, 10395G, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. N. Rao, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Deoxyguanosinetriphosphate Triphosphohydrolase From Pseudomonas Syringae Pv. Phaseolicola 1448A At 2. 35 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PSPPH_2088
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA 1448A
    Organism Taxid: 264730
    Strain: 1448A, RACE 6

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 66)
No.NameCountTypeFull Name
1MSE66Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2PGS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PGS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PGS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PGS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PGS)

(-) Exons   (0, 0)

(no "Exon" information available for 2PGS)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:393
 aligned with Q48JX0_PSE14 | Q48JX0 from UniProtKB/TrEMBL  Length:446

    Alignment length:437
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       
         Q48JX0_PSE14     3 ALDWQTLLNRERLGKTLHSPEELGRSPFHKDHDRIIFSGAFRRLGRKTQVHPVSSNDHIHTRLTHSLEVSCVGRSLGMRVGETLRAALPDWCDPSDLGMVVQSACLAHDIGNPPFGHSGEDAIRNWFNQAAGRGWLDAMSETERNDFLNFEGNAQGFRVLTQLEYHQFDGGTRLTYATLGTYLKYPWTARHADSLGYKKHKFGCYQSELPILEQIAGKLGLPQLEEQRWARHPLVYLMEAADDICYALIDLEDGLEMDLLDYAEVESLLLGLVGDDLPETYRQLGPGDSRRRKLAILRGKAIEHLTNAAARAFVEQQDALLAGTLPGDLVEHMHGPAKRCVLNAKDMARKKIFQDKRKTLHEIGAYTTLEILLNAFCGAAVEQFGGRTPSFKHRRILDLLGNSAPDPKAPLHASFLRMIDFIAGMTDSYASEMAREM 439
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pgsA01 A:2-1             13,A:150-240 Hypothetical        protein af1432                                       2pgsA02 A:114-149,A:354-436         2pgsA01 A:2-113,A:150-240 Hypothetical pro        tein af1432                              2pgsA03 A:241-353 putative deoxygua                nosinetriphosphate triphosphohydrolase like domain            2pgsA02 A:114-149,A:354-436                                                        -- CATH domains
               Pfam domains -------------------------------------------------------------HD-2pgsA01 A:63-178                                                                                                 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............-------------hhhhhhhhhhhhhhhhhhhhh.....-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhh.......--------.........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...----------------hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..........hhhhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pgs A   2 SLDWQTLLNRERL-------------PFHKDHDRIIFSGAFRRLGRKTQVHP-------HTRLTHSLEVSCVGRSLGmRVGETLRAALPDWCDPSDLGmVVQSACLAHDIGNPPFGHSGEDAIRNWFNQAAGRGWLDAmSETERNDFLNFEGNAQGFRVLTQLEYHQFDGGTRLTYATLGTYLKYPWTAR--------KHKFGCYQSELPILEQIAGKLGLPQLEEQRWARHPLVYLmEAADDICYALIDLEDGLEmDLLDYAEVESLLLGLVG----------------RRKLAILRGKAIEHLTNAAARAFVEQQDALLAGTLPGDLVEHmHGPAKRCVLNAKDmARKKIFQDKRKTLHEIGAYTTLEILLNAFCGAAVEQFGGRTPSFKHRRILDLLGNSAPDPKAPLHASFLRmIDFIAGmTDSYASEmAREm 438
                                    11  |      -      | 31        41        51 |      61        71       |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      |261       271   |     -         -|      301       311       321       331  |    341      |351       361       371       381       391       401       411       421    |  431  |   |
                                       14            28                       53      61                79-MSE              100-MSE                                 140-MSE                                            191      200                                    239-MSE            258-MSE          275              292                                       334-MSE       348-MSE                                                                419-MSE  |     434-MSE
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  426-MSE     438-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2PGS)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HD_PDEase (93)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q48JX0_PSE14 | Q48JX0)
molecular function
    GO:0008832    dGTPase activity    Catalysis of the reaction: dGTP + H(2)O = 2'-deoxyguanosine + 2 H(+) + triphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0046039    GTP metabolic process    The chemical reactions and pathways involving GTP, guanosine triphosphate.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2pgs)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pgs)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2pgs
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q48JX0_PSE14 | Q48JX0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q48JX0_PSE14 | Q48JX0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2PGS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PGS)